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Global air temperature increase has caused changes in the global climate such as droughts, floods and severe events. Land cover shifts and the increase in greenhouse gas emissions can intensify these impacts. Therefore, the application of Specific Warming Level 2 (SWL2) technique has been considered to evaluate the global warming issue in various climate scales, which may induce different responses in the climate system. The objective of this study is to evaluate the impacts of a doubling of current atmospheric CO2 concentrations as well as the influence of deforestation of the Amazon Forest on the climate of South America. In this study, the CPTEC-BAM1.2 global model was used to simulate these processes. The first scenario of simulations considered doubled atmospheric CO2 concentration (2XCO2 = 776 ppm) and the second scenario is the total conversion of the Amazon Forest to pasture (DEF). In the third scenario both CO2 and deforestation are considered simultaneously (2XCO2 + DEF). A control simulation considers the natural Amazon Forest shape and a steady CO2 concentration of 388 ppm. Results suggest that the temperature increased in all scenarios, the highest increment in the 2XCO2 + DEF experiment (5.4°C in 2XCO2 + DEF, 5.1°C in DEF and 3.2°C in 2XCO2). The model simulated drastic negative rainfall anomalies in each of three scenarios (2XCO2 + DEF: −2.1 mm day−1, 2XCO2: −1.3 mm day−1 and DEF: −0.9 mm day−1). Besides less precipitation and evapotranspiration, shifts in moisture transport were identified in each of the three scenarios. The effect of doubled atmospheric CO2 produces results similar to deforestation for hydrological water budget changes, and total pasture conversion may intensify such changes.